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Practical Guidelines for ChIP-seq analysis

Overview

ChIP-seq (chromatin Immunoprecipitation followed by sequencing) uses antibodies to determine where a protein binds to a genome.

Analysis

The initial output of ChIP-seq is a set of (short) reads corresponding to the sequences that are bound by a protein. These reads are then run through quality control, then mapped to a genome. The mapping locations do not yet tell us which part of the genome the protein was bound, so Peak Calling must be performed to identify likely regions where the protein is bound (peaks). These peaks are then annotated with relevant information, such as gene start sites, known promoter locations, etc.

One of the goals of ChIP-seq analysis is to find a unique DNA Motif associated with each protein binding site. It is assumed that a Transcription Factor binds to a semi-unique sequence on the genome. By identification of the unique motif, one can associate the bound transcription factor to the unique motif.